Insertion Pipeline
Bowtie2_wholegenome:
  reads:	ISO1-AS-Emb123.fastq.uq.polyn	ISO1-AS-Emb123.filter	percent
uq reads:	158669985	13982844	8.8125%
   reads: 	395719058	71886019	18.1659%
----------------
virus_structural_rna_repbase_filter:
  reads:	ISO1-AS-Emb123.filter	ISO1-AS-Emb123.nostrna	percent
uq reads:	13982844	7619348	54.4907%
   reads: 	71886019	35837110	49.8527%
----------------
TE_filter:
  reads:	ISO1-AS-Emb123.nostrna	ISO1-AS-Emb123.noTE	percent
uq reads:	7619348	7600293	99.7499%
   reads: 	35837110	35798251	99.8916%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-AS-Emb123.noGEN.front	ISO1-AS-Emb123.noGEN.front.gen	percent
uq reads:	7600293	1488883	19.5898%
   reads: 	35798251	5539224	15.4734%
----------------
match_TE:2:
  reads:	ISO1-AS-Emb123.noGEN.front	ISO1-AS-Emb123.noGEN.front.TE	percent
uq reads:	7600293	522871	6.8796%
   reads: 	35798251	1552113	4.3357%
----------------
match_dm6_mask_gen:1:
  reads:	ISO1-AS-Emb123.noGEN.end	ISO1-AS-Emb123.noGEN.end.gen	percent
uq reads:	7600293	1402801	18.4572%
   reads: 	35798251	5396684	15.0753%
----------------
match_TE:2:
  reads:	ISO1-AS-Emb123.noGEN.end	ISO1-AS-Emb123.noGEN.end.TE	percent
uq reads:	7600293	579900	7.6300%
   reads: 	35798251	1790622	5.0020%
----------------
Candidate insertion sites in file: ISO1-AS-Emb123_insert.txt
  reads:	92883
  uqreads:	37296
  Number of Candidate sites:	37296

Level 1 collapse of insertion sites in file: ISO1-AS-Emb123_insert_base22_W300_level1.xls
  Number of Level 1 collapsed sites:	222

Level 1 annotation file: ISO1-AS-Emb123_level1siteannotation.xls
Insertion sites in fixed bin:
ISO1-AS-Emb123_insert_fixed_bin_5000.txt
End of pipeline


Beginning of Depletion Pipeline
match_dm6_mask_gen_del:1:
  reads:	ISO1-AS-Emb123.noGEN.front	ISO1-AS-Emb123.noGEN.front.gendel	percent
uq reads:	7600293	1488883	19.5898%
   reads: 	35798251	5539224	15.4734%
----------------
match_dm6_mask_gen_del:1:
  reads:	ISO1-AS-Emb123.noGEN.end	ISO1-AS-Emb123.noGEN.end.gendel	percent
uq reads:	7600293	1402801	18.4572%
   reads: 	35798251	5396684	15.0753%
----------------
Candidate breakpoint sites in file: ISO1-AS-Emb123_depletion.xls
  reads:	44961
  uqreads:	16873
  Number of reads supporting candidate sites:	16873

Level 1 collapse of depletion sites in file: ISO1-AS-Emb123_depletion_level1.xls
  Number of Level 1 collapsed sites:	432